New version of phenogram with user control of axis dimensions

An anonymous user request was recently made to add the potential to control the axis dimensions in phenogram. I guessed (correctly) that this would not be too hard, and so I have added this capability to the newest version of the function (direct link to code here).

To accomplish this, I have just added one additional argument:

> args(phenogram)
function (tree, x, fsize = 1, ftype = "reg", colors = NULL, axes = list())
NULL

This is specified as a list containing two components: trait and time. The former should be a vector of length 2 specifying the dimensions of the vertical (trait) axis; and the latter a vector of length 2 giving the desired dimensions on the horizontal (time since the root) axis.

Within the function itself, I have now added the following lines of code (before calling plot.window to create the graph):

plot.new()
if(is.null(axes$trait)) ylim<-c(min(x),max(x))
else ylim<-axes$trait
if(is.null(axes$time))
   xlim<-c(min(H),max(H)+fsize*max(strwidth(tree$tip.label)))
else
   xlim<-c(axes$time[1],axes$time[2]+fsize*max(strwidth(tree$tip.label)))
plot.window(ylim=ylim,xlim=xlim)

This code just uses the vectors provide in axes to specify the dimensions in x & y for the plot - or, if none have been provided, it uses the range of x and nodeHeights(tree) (plus a little bit of extra space to print tip labels).

Let's see how it works:

> source("phenogram.R")
> tree<-pbtree(n=10)
> x<-fastBM(tree)
> phenogram(tree,x) # default settings

> phenogram(tree,x,axes=list(trait=c(-2,2))) # change vertical

> # change horizontal
> phenogram(tree,x,axes=list(trait=c(-2,2), time=c(1.5,max(nodeHeights(tree)))))

It also works with a mapped discrete character. For instance:

> Q<-matrix(c(-2,2,2,-2),2,2)
> mtree<-sim.history(tree,Q)
> cols<-c("blue","red"); names(cols)<-c(1,2)
> phenogram(mtree,x,colors=cols,axes=list(trait=c(-2,2)))

Cool.